CHANGELOG.md

@@ -2,6 +2,26 @@
 
 ## Unreleased
 
+### Correctness: edits planned from another file after a rename or `chdir` (2026-09-27)
+- **`FileEditor` planned each edit by re-opening its path but wrote
+  through the file it held open** (fixed 2026-09-27; on main since PR #18,
+  no release). When the path came to name another file between edits — a
+  rename or replacement, or, for a relative path, a change of working
+  directory — an edit was laid out from the other file's metadata and
+  written into the held one, corrupting it (h5py: "invalid dataset size,
+  likely file corruption"). The Python `'r+'` handle had the same flaw in
+  its reads: it reopened the path after every edit, so reads came from the
+  other file. The editor now plans every edit from the file it holds, and
+  its path is canonicalised at open. New `FileEditor::reader()` opens the
+  held file anew for reading (on Linux through `/proc/self/fd`, so it
+  follows a renamed file; elsewhere by the path, refused when the path no
+  longer names the held file), without sharing the editor's lock; the
+  Python handle reads through it, and a `'w'` file is written at the
+  absolute path it was opened with. Tests: `edit_tests.rs`'s
+  `edits_go_to_the_file_held_not_the_path`; `test_edit.py`'s
+  `test_relative_path_and_chdir` and `test_path_replaced_between_edits`
+  (the review's repro).
+
 ### Correctness: zero extents in Fixed/Extensible Array chunk indexes (2026-09-27)
 - **A chunked dataset whose maximum (or, with none recorded, current)
   extent is 0 along a dimension made the reader divide by zero** (fixed

crates/clawhdf5-io/src/mmap.rs

@@ -39,6 +39,23 @@ impl MmapReader {
         Ok(Self { _file: file, mmap })
     }
 
+    /// Memory-map a file that is already open (for reading).
+    ///
+    /// The mapping references `file`'s open file description for as long as
+    /// it lives, so a `flock` taken through that description (or a
+    /// `try_clone` of it) is held until the reader is dropped.
+    ///
+    /// # Safety
+    ///
+    /// The same contract as [`open`](Self::open): the file must not be
+    /// modified while the mapping is active.
+    pub fn from_file(file: fs::File) -> io::Result<Self> {
+        // SAFETY: a read-only mapping; the caller keeps the file unmodified
+        // while it is alive.
+        let mmap = unsafe { Mmap::map(&file)? };
+        Ok(Self { _file: file, mmap })
+    }
+
     /// Zero-copy access to the entire file contents.
     pub fn as_bytes(&self) -> &[u8] {
         &self.mmap

crates/clawhdf5-py/src/file.rs

@@ -110,7 +110,9 @@ impl PyFile {
             "w" => Ok(Self {
                 filename,
                 inner: Some(FileInner::Write(WriteState {
-                    path: PathBuf::from(path),
+                    // Absolute now: the file is written at close, possibly
+                    // after the working directory changed.
+                    path: std::path::absolute(path).unwrap_or_else(|_| PathBuf::from(path)),
                     root_datasets: Vec::new(),
                     root_attrs: Arc::new(Mutex::new(Vec::new())),
                     groups: Vec::new(),

crates/clawhdf5-py/src/handle.rs

@@ -8,7 +8,8 @@
 //!
 //! A file opened with `'r+'` also holds a [`FileEditor`]. An edit takes the
 //! file's write lock, so no read runs while the file changes underneath it,
-//! and reopens the file afterwards: reads after an edit see the new bytes
+//! and reopens the file afterwards, through the editor's own open file
+//! rather than its path: reads after an edit see the new bytes
 //! (a grown file, a new dataspace), never a stale mapping or chunk cache.
 //! Objects that cache something an edit can change compare
 //! [`Handle::generation`] with the value they cached it at.
@@ -16,7 +17,6 @@
 //! Lock discipline (no deadlock with the GIL): the file lock is only taken
 //! with the GIL released, and code that holds it never touches Python.
 
-use std::path::PathBuf;
 use std::sync::atomic::{AtomicU64, Ordering};
 use std::sync::{Arc, Mutex, PoisonError, RwLock};
 
@@ -28,8 +28,9 @@ use crate::{panic_text, to_py_err};
 
 /// Where the file's bytes come from.
 pub(crate) enum Source {
-    /// A local path (memory-mapped).
-    Local(PathBuf),
+    /// A local file (memory-mapped). Its path is not kept: nothing reopens
+    /// it by path (see `open_editable`).
+    Local,
     /// A URL, read through `clawhdf5-remote`'s block cache.
     Remote {
         url: String,
@@ -74,25 +75,23 @@ impl Handle {
     /// A local file, read-only.
     pub(crate) fn open_local(py: Python<'_>, path: &str) -> PyResult<Arc<Self>> {
         let file = py.detach(|| crate::no_panic(|| File::open(path).map_err(to_py_err)))?;
-        Ok(Self::new(file, Source::Local(PathBuf::from(path)), None))
+        Ok(Self::new(file, Source::Local, None))
     }
 
     /// A local file, open for in-place editing (`'r+'`): the editor takes
     /// the file's exclusive lock and checks that it can edit the file, then
-    /// the file is opened for reading.
+    /// the file is read through the editor's own file — never by path
+    /// again, so a later `os.chdir` or a rename or replacement of the path
+    /// cannot make reads (or the editor's plans) come from another file.
     pub(crate) fn open_editable(py: Python<'_>, path: &str) -> PyResult<Arc<Self>> {
         let (file, editor) = py.detach(|| {
             crate::no_panic(|| {
                 let editor = FileEditor::open(path).map_err(to_py_err)?;
-                let file = File::open(path).map_err(to_py_err)?;
+                let file = editor.reader().map_err(to_py_err)?;
                 Ok((file, editor))
             })
         })?;
-        Ok(Self::new(
-            file,
-            Source::Local(PathBuf::from(path)),
-            Some(editor),
-        ))
+        Ok(Self::new(file, Source::Local, Some(editor)))
     }
 
     /// A remote file (`http(s)://`, `s3://`, ...).
@@ -153,7 +152,7 @@ impl Handle {
     pub(crate) fn remote_storage(&self) -> Option<&clawhdf5_remote::RemoteStorage> {
         match &self.source {
             Source::Remote { storage, .. } => Some(storage),
-            Source::Local(_) => None,
+            Source::Local => None,
         }
     }
 
@@ -161,7 +160,7 @@ impl Handle {
     pub(crate) fn redacted_url(&self) -> Option<String> {
         match &self.source {
             Source::Remote { url, .. } => Some(clawhdf5_remote::redact_url(url)),
-            Source::Local(_) => None,
+            Source::Local => None,
         }
     }
 
@@ -185,14 +184,12 @@ impl Handle {
         let Some(editor) = &self.editor else {
             return Err(PyOSError::new_err(match self.source {
                 Source::Remote { .. } => "remote files are read-only",
-                Source::Local(_) => {
-                    "the file is open read-only; open it with mode 'r+' to change it"
-                }
+                Source::Local => "the file is open read-only; open it with mode 'r+' to change it",
             }));
         };
-        let Source::Local(path) = &self.source else {
+        if matches!(self.source, Source::Remote { .. }) {
             return Err(PyOSError::new_err("remote files are read-only"));
-        };
+        }
         py.detach(|| {
             let mut ed = editor.lock().unwrap_or_else(PoisonError::into_inner);
             let ed = ed
@@ -202,7 +199,8 @@ impl Handle {
             let result = std::panic::catch_unwind(std::panic::AssertUnwindSafe(|| f(ed)));
             // Drop the old mapping and its chunk cache before reopening.
             *file = None;
-            let reopened = std::panic::catch_unwind(|| File::open(path));
+            // Through the editor's file, not the path (see `open_editable`).
+            let reopened = std::panic::catch_unwind(std::panic::AssertUnwindSafe(|| ed.reader()));
             self.generation.fetch_add(1, Ordering::AcqRel);
             match reopened {
                 Ok(Ok(f)) => *file = Some(f),

crates/clawhdf5-py/tests/test_edit.py

@@ -823,3 +823,76 @@ def test_close_releases_the_file(h5py, tmp_path):
         ds[0] = 1
     with h5py.File(path, "r+") as g:
         g["d"][0] = 9
+
+
+def _two_files(h5py, tmp_path):
+    """d1/f.h5 and d2/f.h5: same name, different layouts (the review's
+    repro)."""
+    (tmp_path / "d1").mkdir()
+    (tmp_path / "d2").mkdir()
+    with h5py.File(tmp_path / "d1" / "f.h5", "w") as f:
+        f.create_dataset("x", data=np.arange(10, dtype="<i4"))
+        f.create_dataset("big", data=np.full(5000, 1.5))
+    with h5py.File(tmp_path / "d2" / "f.h5", "w") as f:
+        f.create_dataset("pad", data=np.full(3000, 2.5))
+        f.create_dataset("x", data=np.arange(10, dtype="<i4") + 500)
+    return tmp_path / "d1" / "f.h5", tmp_path / "d2" / "f.h5"
+
+
+def _held_file_edited(h5py, held, other, other_bytes):
+    """The edits went to `held`, planned from its own metadata; `other`
+    was not touched."""
+    assert other.read_bytes() == other_bytes, "the other file changed"
+    with h5py.File(held, "r") as f:
+        np.testing.assert_array_equal(f["x"][()], np.full(10, 7))
+        np.testing.assert_array_equal(f["big"][()], np.full(5000, 1.5))
+        np.testing.assert_array_equal(f.attrs["note"], np.arange(50.0))
+    h5dump_reads(str(held))
+
+
+def test_relative_path_and_chdir(h5py, tmp_path, monkeypatch):
+    """A file opened by a relative path keeps being the file edited and read
+    after os.chdir (an edit was planned from the file the path named in the
+    new directory and written into the one open, corrupting it)."""
+    held, other = _two_files(h5py, tmp_path)
+    other_bytes = other.read_bytes()
+    monkeypatch.chdir(held.parent)
+    f = clawhdf5.File("f.h5", "r+")
+    ds = f["x"]
+    monkeypatch.chdir(other.parent)
+    ds[:] = np.full(10, 7, "<i4")
+    np.testing.assert_array_equal(ds[:5], np.full(5, 7))  # read from the held file
+    f.attrs["note"] = np.arange(50.0)
+    np.testing.assert_array_equal(f["big"][()], np.full(5000, 1.5))
+    assert "pad" not in f
+    f.close()
+    _held_file_edited(h5py, held, other, other_bytes)
+    # 'w' writes where the path named when the file was opened.
+    monkeypatch.chdir(held.parent)
+    w = clawhdf5.File("new.h5", "w")
+    monkeypatch.chdir(other.parent)
+    w.create_dataset("d", data=np.arange(3))
+    w.close()
+    assert (held.parent / "new.h5").exists() and not (other.parent / "new.h5").exists()
+
+
+def test_path_replaced_between_edits(h5py, tmp_path):
+    """The path renamed away and another file put in its place between
+    edits: the edits go to the file held open, never mixed with the other."""
+    held, other = _two_files(h5py, tmp_path)
+    path = str(tmp_path / "f.h5")
+    os.replace(held, path)
+    moved = tmp_path / "moved.h5"
+    with clawhdf5.File(path, "r+") as f:
+        ds = f["x"]
+        ds[0] = 7
+        os.replace(path, moved)
+        shutil.copy(other, path)
+        other_bytes = open(path, "rb").read()
+        ds[:] = np.full(10, 7, "<i4")
+        f.attrs["note"] = np.arange(50.0)
+        np.testing.assert_array_equal(f["x"][()], np.full(10, 7))
+        assert "pad" not in f
+    from pathlib import Path
+    _held_file_edited(h5py, moved, Path(path), other_bytes)
+

crates/clawhdf5/src/edit/mod.rs

@@ -65,7 +65,8 @@ const MSG_FLAG_DONTSHARE: u8 = 0x04;
 /// that may be mid-update.
 ///
 /// Every method is one self-contained edit: it re-reads the file's
-/// metadata, applies the change, and syncs the file before returning.
+/// metadata (from the file it holds open, never by path), applies the
+/// change, and syncs the file before returning.
 ///
 /// # What it can change
 ///
@@ -750,9 +751,17 @@ impl FileEditor {
     /// consistent: a metadata cache image, paged or persistent free-space
     /// management, a multi-file driver, a file another writer has marked
     /// open (superblock version 3 consistency flags).
+    ///
+    /// The path is only used to open the file: every edit is planned from
+    /// and written to the file opened here, even if the path is renamed,
+    /// replaced or (relative) resolved from another working directory
+    /// later. [`path`](Self::path) is the absolute path it had at open.
     pub fn open<P: AsRef<Path>>(path: P) -> Result<Self, Error> {
-        let path = path.as_ref().to_path_buf();
-        let file = OpenOptions::new().read(true).write(true).open(&path)?;
+        let file = OpenOptions::new()
+            .read(true)
+            .write(true)
+            .open(path.as_ref())?;
+        let path = std::fs::canonicalize(path.as_ref())?;
         match file.try_lock() {
             Ok(()) => {}
             Err(TryLockError::WouldBlock) => {
@@ -768,16 +777,68 @@ impl FileEditor {
             file,
             free: FreeList::default(),
         };
-        let f = File::open(&ed.path)?;
+        let f = ed.plan_reader()?;
         check_editable(&f)?;
         Ok(ed)
     }
 
-    /// The file's path.
+    /// The file's absolute path when it was opened (it may have been
+    /// renamed since; the editor keeps editing the file it opened).
     pub fn path(&self) -> &Path {
         &self.path
     }
 
+    /// A reader over the file this editor holds, as last written: the file
+    /// opened by [`open`](Self::open), not whatever its path names now.
+    ///
+    /// It opens the file anew (read-only), so it does not share the
+    /// editor's lock and stays usable after the editor is dropped: on Linux
+    /// through `/proc/self/fd`, which reaches the held file even after its
+    /// path was renamed or replaced; elsewhere by the path the file had at
+    /// open, refused with [`Error::Io`] when that path no longer names the
+    /// held file (on Unix, compared by device and inode; Windows cannot
+    /// check). With the `mmap` feature the reader maps the file: edits
+    /// through the editor change the bytes it sees, so take a new reader
+    /// after each edit rather than reading through an old one while an edit
+    /// runs.
+    pub fn reader(&self) -> Result<File, Error> {
+        let dir = self.path.parent().map(Path::to_path_buf);
+        File::from_std_file(self.reopen()?, dir)
+    }
+
+    /// A new read-only open file description of the held file (see
+    /// [`reader`](Self::reader)).
+    fn reopen(&self) -> Result<std::fs::File, Error> {
+        #[cfg(target_os = "linux")]
+        {
+            use std::os::fd::AsRawFd;
+            let proc = format!("/proc/self/fd/{}", self.file.as_raw_fd());
+            if let Ok(f) = std::fs::File::open(proc) {
+                return Ok(f);
+            }
+        }
+        let f = std::fs::File::open(&self.path)?;
+        #[cfg(unix)]
+        {
+            use std::os::unix::fs::MetadataExt;
+            let (a, b) = (self.file.metadata()?, f.metadata()?);
+            if (a.dev(), a.ino()) != (b.dev(), b.ino()) {
+                return Err(Error::Io(std::io::Error::other(format!(
+                    "{} no longer names the file being edited (renamed or replaced)",
+                    self.path.display()
+                ))));
+            }
+        }
+        Ok(f)
+    }
+
+    /// A reader over the held file itself for planning an edit (it shares
+    /// the file's lock, and is dropped before the edit writes).
+    fn plan_reader(&self) -> Result<File, Error> {
+        let dir = self.path.parent().map(Path::to_path_buf);
+        File::from_std_file(self.file.try_clone()?, dir)
+    }
+
     /// Bytes earlier edits of this editor freed that later ones can still
     /// reuse.
     pub fn reusable_bytes(&self) -> u64 {
@@ -794,7 +855,7 @@ impl FileEditor {
         &mut self,
         op: impl FnOnce(&File, &mut Image<'_>) -> Result<R, Error>,
     ) -> Result<R, Error> {
-        let f = File::open(&self.path)?;
+        let f = self.plan_reader()?;
         check_editable(&f)?;
         let sb = f.superblock().clone();
         let user_block = f.user_block_size();

crates/clawhdf5/src/reader.rs

@@ -405,6 +405,38 @@ impl File {
         }
     }
 
+    /// A reader over an already open file (the file itself, not whatever
+    /// its path names now): mapped with the `mmap` feature, else read into
+    /// memory. `base_dir` resolves external Virtual Dataset sources.
+    pub(crate) fn from_std_file(
+        file: std::fs::File,
+        base_dir: Option<std::path::PathBuf>,
+    ) -> Result<Self, Error> {
+        #[cfg(feature = "mmap")]
+        let mut f = {
+            let reader = clawhdf5_io::MmapReader::from_file(file).map_err(Error::Io)?;
+            let (data, superblock) = FileData::new(Backing::Mmap(reader))?;
+            Self {
+                data,
+                superblock,
+                chunk_cache: ChunkCache::new(),
+                base_dir: None,
+                vds_resolver: None,
+            }
+        };
+        #[cfg(not(feature = "mmap"))]
+        let mut f = {
+            use std::io::{Read, Seek, SeekFrom};
+            let mut file = file;
+            let mut bytes = Vec::new();
+            file.seek(SeekFrom::Start(0)).map_err(Error::Io)?;
+            file.read_to_end(&mut bytes).map_err(Error::Io)?;
+            Self::from_bytes(bytes)?
+        };
+        f.base_dir = base_dir;
+        Ok(f)
+    }
+
     /// Open an HDF5 file by reading it entirely into memory.
     ///
     /// This is the pre-mmap behaviour and is useful when memory-mapping is

crates/clawhdf5/tests/edit_tests.rs

@@ -162,3 +162,59 @@ fn shrink_then_grow_reads_fill() {
     raw[..4].fill(0.5);
     assert_eq!(f.dataset("raw").unwrap().read_f64().unwrap(), raw);
 }
+
+/// The editor plans every edit from the file it holds open, never by
+/// re-opening its path: with the path renamed away and another file put in
+/// its place, edits go to the held file, planned from its own metadata,
+/// and the file now at the path is untouched (planning from it and writing
+/// into the held file corrupted the held one).
+#[test]
+fn edits_go_to_the_file_held_not_the_path() {
+    let dir = tempfile::tempdir().unwrap();
+    let a = dir.path().join("a.h5");
+    let b = dir.path().join("b.h5");
+    let mut fb = FileBuilder::new();
+    fb.create_dataset("x")
+        .with_i32_data(&[0; 10])
+        .with_shape(&[10]);
+    fb.create_dataset("big")
+        .with_f64_data(&[1.5; 5000])
+        .with_shape(&[5000]);
+    fb.set_attr("title", AttrValue::String("a".into()));
+    fb.write(&a).unwrap();
+    let mut fb = FileBuilder::new();
+    fb.create_dataset("pad")
+        .with_f64_data(&[2.5; 3000])
+        .with_shape(&[3000]);
+    fb.create_dataset("x")
+        .with_i32_data(&[500; 10])
+        .with_shape(&[10]);
+    fb.write(&b).unwrap();
+
+    let mut ed = FileEditor::open(&a).unwrap();
+    assert!(ed.path().is_absolute());
+    let moved = dir.path().join("moved.h5");
+    std::fs::rename(&a, &moved).unwrap();
+    std::fs::rename(&b, &a).unwrap();
+    let other = std::fs::read(&a).unwrap();
+
+    ed.write_values("x", &Selection::All, &[7i32; 10]).unwrap();
+    let vals: Vec<f64> = (0..50).map(f64::from).collect();
+    ed.set_attr("/", "note", &AttrValue::F64Array(vals.clone()))
+        .unwrap();
+    // The editor's own reader sees the held file.
+    let r = ed.reader().unwrap();
+    assert_eq!(r.dataset("x").unwrap().read_i32().unwrap(), [7; 10]);
+    assert!(r.dataset("pad").is_err());
+    drop(r);
+    drop(ed);
+
+    assert!(
+        std::fs::read(&a).unwrap() == other,
+        "the file at the path changed"
+    );
+    let f = File::open(&moved).unwrap();
+    assert_eq!(f.dataset("x").unwrap().read_i32().unwrap(), [7; 10]);
+    assert_eq!(f.dataset("big").unwrap().read_f64().unwrap(), [1.5; 5000]);
+    assert!(matches!(f.root().attr("note").unwrap(), Some(AttrValue::F64Array(v)) if v == vals));
+}

docs/known-issues.md

@@ -143,6 +143,12 @@ space it leaves is too small for its next, larger version.
 **No journal.** A crash while an edit patches existing structures can leave
 the file inconsistent; see the `FileEditor` documentation.
 
+**Renamed files outside Linux.** Edits always go to the file the editor
+opened. `FileEditor::reader()` (which the Python `'r+'` handle reads
+through) reopens it through `/proc/self/fd` on Linux; elsewhere it reopens
+the path, and after the path was renamed or replaced it fails (on Unix;
+Windows cannot tell and would read whatever the path names).
+
 ## Python in-place editing (`clawhdf5.File(path, 'r+')`) limits
 
 **Status:** open (added 2026-09-27). The Python bindings edit through